data_VNP # _chem_comp.id VNP _chem_comp.name ;3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-(2-{[HYDROXY(PHOSPHONOAMINO)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-I UM ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H20 N5 O6 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;THIAMIN-PNP; [2-[3-[(4-AMINO-2-METHYL-PYRIMIDIN-5-YL)METHYL]-4-METHYL-1-THIA-3-AZON IACYCLOPENTA-2,4-DIEN-5-YL]ETHOXY-HYDROXY-PHOSPHORYL]AMINOPHOSPHONIC ACID ; _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2006-03-14 _chem_comp.pdbx_modified_date 2020-06-17 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 424.330 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VNP _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 2G9Z _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal VNP O2G O2G O 0 1 N N N 30.659 74.774 7.143 6.839 1.077 -0.553 O2G VNP 1 VNP PG PG P 0 1 N N N 29.093 75.082 7.352 5.807 1.048 0.683 PG VNP 2 VNP O3G O3G O 0 1 N N N 28.843 76.535 6.713 6.114 -0.108 1.555 O3G VNP 3 VNP O1G O1G O 0 1 N N N 28.716 75.065 8.784 5.947 2.410 1.530 O1G VNP 4 VNP N3B N3B N 0 1 N N N 28.252 73.992 6.489 4.235 0.909 0.099 N3B VNP 5 VNP PB PB P 0 1 N N S 28.128 74.346 4.909 4.046 -0.505 -0.794 PB VNP 6 VNP O2B O2B O 0 1 N N N 27.558 73.173 4.209 4.339 -1.674 0.066 O2B VNP 7 VNP O1B O1B O 0 1 N N N 29.441 74.848 4.450 5.062 -0.491 -2.043 O1B VNP 8 VNP O1 O1 O 0 1 N N N 27.077 75.566 4.858 2.533 -0.601 -1.333 O1 VNP 9 VNP C7 C7 C 0 1 N N N 25.722 75.479 5.316 1.415 -0.842 -0.477 C7 VNP 10 VNP C12 C12 C 0 1 N N N 24.924 76.488 4.489 0.131 -0.872 -1.309 C12 VNP 11 VNP C11 C11 C 0 1 Y N N 23.457 76.702 4.877 -1.048 -1.126 -0.406 C11 VNP 12 VNP C10 C10 C 0 1 Y N N 23.199 77.559 6.119 -1.782 -0.194 0.209 C10 VNP 13 VNP CM4 CM4 C 0 1 N N N 24.136 78.688 6.555 -1.510 1.281 0.069 CM4 VNP 14 VNP S1 S1 S 0 1 Y N N 22.453 75.235 5.281 -1.707 -2.704 0.020 S1 VNP 15 VNP C9 C9 C 0 1 Y N N 21.450 76.128 6.402 -2.899 -1.954 0.989 C9 VNP 16 VNP N5 N5 N 1 1 Y N N 22.099 77.224 6.801 -2.763 -0.671 0.948 N5 VNP 17 VNP C7A C7A C 0 1 N N N 21.693 77.992 7.989 -3.662 0.216 1.690 C7A VNP 18 VNP C5A C5A C 0 1 Y N N 20.198 77.893 8.307 -4.777 0.674 0.784 C5A VNP 19 VNP C6A C6A C 0 1 Y N N 19.866 77.343 9.539 -4.692 1.875 0.108 C6A VNP 20 VNP N1A N1A N 0 1 Y N N 18.612 77.295 9.948 -5.691 2.245 -0.681 N1A VNP 21 VNP C2A C2A C 0 1 Y N N 17.620 77.774 9.185 -6.757 1.485 -0.827 C2A VNP 22 VNP CM2 CM2 C 0 1 N N N 16.181 77.737 9.705 -7.867 1.949 -1.735 CM2 VNP 23 VNP N3A N3A N 0 1 Y N N 17.889 78.306 7.985 -6.880 0.332 -0.202 N3A VNP 24 VNP C4A C4A C 0 1 Y N N 19.149 78.376 7.530 -5.918 -0.110 0.603 C4A VNP 25 VNP N4A N4A N 0 1 N N N 19.374 78.916 6.335 -6.049 -1.325 1.255 N4A VNP 26 VNP H2G H2G H 0 1 N N N 30.849 74.713 6.214 6.696 1.810 -1.167 H2G VNP 27 VNP H1G H1G H 0 1 N N N 29.501 75.061 9.319 6.829 2.556 1.898 H1G VNP 28 VNP H3B H3B H 0 1 N N N 28.716 73.110 6.571 3.565 0.953 0.852 H3B VNP 29 VNP H1B H1B H 0 1 N N N 29.427 74.956 3.506 4.928 0.250 -2.650 H1B VNP 30 VNP H71 H71 H 0 1 N N N 25.329 74.462 5.168 1.543 -1.799 0.028 H71 VNP 31 VNP H72 H72 H 0 1 N N N 25.650 75.699 6.391 1.347 -0.046 0.265 H72 VNP 32 VNP H121 H121 H 0 0 N N N 25.429 77.460 4.592 0.003 0.085 -1.814 H121 VNP 33 VNP H122 H122 H 0 0 N N N 24.897 76.071 3.471 0.199 -1.668 -2.051 H122 VNP 34 VNP HM41 HM41 H 0 0 N N N 24.361 78.585 7.627 -2.074 1.676 -0.776 HM41 VNP 35 VNP HM42 HM42 H 0 0 N N N 25.071 78.632 5.978 -1.814 1.795 0.981 HM42 VNP 36 VNP HM43 HM43 H 0 0 N N N 23.650 79.658 6.374 -0.445 1.440 -0.099 HM43 VNP 37 VNP H9 H9 H 0 1 N N N 20.460 75.838 6.721 -3.659 -2.477 1.550 H9 VNP 38 VNP H7A1 H7A1 H 0 0 N N N 22.252 77.604 8.853 -4.082 -0.320 2.541 H7A1 VNP 39 VNP H7A2 H7A2 H 0 0 N N N 21.909 79.050 7.779 -3.105 1.083 2.046 H7A2 VNP 40 VNP H6A H6A H 0 1 N N N 20.647 76.948 10.172 -3.822 2.505 0.221 H6A VNP 41 VNP HM21 HM21 H 0 0 N N N 16.188 77.728 10.805 -7.687 1.583 -2.746 HM21 VNP 42 VNP HM22 HM22 H 0 0 N N N 15.640 78.626 9.349 -8.819 1.560 -1.372 HM22 VNP 43 VNP HM23 HM23 H 0 0 N N N 15.681 76.830 9.335 -7.899 3.038 -1.743 HM23 VNP 44 VNP H4A1 H4A1 H 0 0 N N N 19.430 79.910 6.423 -5.344 -1.638 1.843 H4A1 VNP 45 VNP H4A2 H4A2 H 0 0 N N N 20.235 78.565 5.967 -6.845 -1.863 1.123 H4A2 VNP 46 # # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal VNP O2G PG SING N N 1 VNP O2G H2G SING N N 2 VNP PG O3G DOUB N N 3 VNP PG O1G SING N N 4 VNP PG N3B SING N N 5 VNP O1G H1G SING N N 6 VNP N3B PB SING N N 7 VNP N3B H3B SING N N 8 VNP PB O2B DOUB N N 9 VNP PB O1B SING N N 10 VNP PB O1 SING N N 11 VNP O1B H1B SING N N 12 VNP O1 C7 SING N N 13 VNP C7 C12 SING N N 14 VNP C7 H71 SING N N 15 VNP C7 H72 SING N N 16 VNP C12 C11 SING N N 17 VNP C12 H121 SING N N 18 VNP C12 H122 SING N N 19 VNP C11 C10 DOUB Y N 20 VNP C11 S1 SING Y N 21 VNP C10 CM4 SING N N 22 VNP C10 N5 SING Y N 23 VNP CM4 HM41 SING N N 24 VNP CM4 HM42 SING N N 25 VNP CM4 HM43 SING N N 26 VNP S1 C9 SING Y N 27 VNP C9 N5 DOUB Y N 28 VNP C9 H9 SING N N 29 VNP N5 C7A SING N N 30 VNP C7A C5A SING N N 31 VNP C7A H7A1 SING N N 32 VNP C7A H7A2 SING N N 33 VNP C5A C6A DOUB Y N 34 VNP C5A C4A SING Y N 35 VNP C6A N1A SING Y N 36 VNP C6A H6A SING N N 37 VNP N1A C2A DOUB Y N 38 VNP C2A CM2 SING N N 39 VNP C2A N3A SING Y N 40 VNP CM2 HM21 SING N N 41 VNP CM2 HM22 SING N N 42 VNP CM2 HM23 SING N N 43 VNP N3A C4A DOUB Y N 44 VNP C4A N4A SING N N 45 VNP N4A H4A1 SING N N 46 VNP N4A H4A2 SING N N 47 # # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor VNP SMILES ACDLabs 10.04 "O=P(O)(O)NP(=O)(O)OCCc1sc[n+](c1C)Cc2c(nc(nc2)C)N" VNP SMILES_CANONICAL CACTVS 3.341 "Cc1ncc(C[n+]2csc(CCO[P@](O)(=O)N[P](O)(O)=O)c2C)c(N)n1" VNP SMILES CACTVS 3.341 "Cc1ncc(C[n+]2csc(CCO[P](O)(=O)N[P](O)(O)=O)c2C)c(N)n1" VNP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO[P@](=O)(NP(=O)(O)O)O" VNP SMILES "OpenEye OEToolkits" 1.5.0 "Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(NP(=O)(O)O)O" VNP InChI InChI 1.03 "InChI=1S/C12H19N5O6P2S/c1-8-11(3-4-23-25(21,22)16-24(18,19)20)26-7-17(8)6-10-5-14-9(2)15-12(10)13/h5,7H,3-4,6H2,1-2H3,(H5-,13,14,15,16,18,19,20,21,22)/p+1" VNP InChIKey InChI 1.03 LWNISHVQCROCTL-UHFFFAOYSA-O # # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier VNP "SYSTEMATIC NAME" ACDLabs 10.04 "3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonoamino)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium" VNP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[2-[3-[(4-amino-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-3-ium-5-yl]ethoxy-hydroxy-phosphoryl]amino]phosphonic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site VNP "Create component" 2006-03-14 RCSB VNP "Modify descriptor" 2011-06-04 RCSB VNP "Modify synonyms" 2020-06-05 PDBE # # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 VNP THIAMIN-PNP ? ? 2 VNP "[2-[3-[(4-AMINO-2-METHYL-PYRIMIDIN-5-YL)METHYL]-4-METHYL-1-THIA-3-AZON IACYCLOPENTA-2,4-DIEN-5-YL]ETHOXY-HYDROXY-PHOSPHORYL]AMINOPHOSPHONIC ACID" ? ? ##